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[[Category:RAREMETALWORKER]]
'''RAREMETALWORKER''' is a tool for generating summary statistics for rare variants and gene level meta analyses using [http://genome.sph.umich.edu/wiki/RAREMETAL '''RAREMETAL'''].
'''RAREMETALWORKER''' is a tool for single variant analysis, generating summary statistics for gene level meta analyses in [http://genome.sph.umich.edu/wiki/RAREMETAL '''RAREMETAL'''].
If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].
If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].
If you have any questions, please contact [[Shuang Feng|'''Shuang Feng''']] sfengsph at umich dot edu or [[Goncalo_Abecasis | '''Goncalo Abecasis''']] goncalo at umich dot edu.
If you have any questions, please contact Sai Chen (saichen at umich dot edu) or [[Goncalo_Abecasis | '''Goncalo Abecasis''']] (goncalo at umich dot edu).
* The [[RAREMETALWORKER_method | '''RAREMETALWORKER method''']]
* The [[RAREMETALWORKER_method | '''RAREMETALWORKER method''']]
* The [[Tutorial:_RAREMETAL| '''RAREMETALWORKER quick start tutorial''']]
* The [[Tutorial:_RAREMETAL| '''RAREMETALWORKER quick start tutorial''']]
* The [[RAREMETALWORKER_SPECIAL_TOPICS | '''RAREMETALWORKER special topics''']]
* The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]
* The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]
* The [[RAREMETAL FAQ | '''FAQ''']]
* The [[RAREMETAL FAQ | '''FAQ''']]
* The [[RAREMETAL_Change_Log | '''Change Log''']]
== Key Features ==
== Key Features ==
== Software Download and Installation ==
== Software Download and Installation ==
=== Where to Download ===
=== DOWNLOAD ===
We have tested compilation on several platforms including Linux, MAC OS X, and Windows.
For source code and executables together with instructions of building from source, please go to [[RAREMETAL_DOWNLOAD_%26_BUILD |'''DOWNLOAD source and executables''']].
For questions about building and compilation, please go to [[RAREMETAL_FAQ | '''FAQ''']].
For compiling questions, please go to [http://genome.sph.umich.edu/wiki/RAREMETAL_FAQ ''' FAQ'''] for more information.
=== How to Execute ===
=== How to Execute ===
Method description and key formulae can be found in [http://genome.sph.umich.edu/wiki/RAREMETALWORKER_method '''RAREMETALWORKER METHOD'''].
Method description and key formulae can be found in [http://genome.sph.umich.edu/wiki/RAREMETALWORKER_method '''RAREMETALWORKER METHOD'''].
==For Binary Traits==
RAREMETALWORKER currently treat all traits as quantitative. If your trait is binary, the odds ratio can be approximated from effect size estimates generated by RAREMETALWORKER. The installation/source package has a script included to augment the odds ratio estimates to the last column of the RAREMETALWORKER output. For details, please refer to [[RAREMETAL_DOWNLOAD_%26_BUILD#Calculating_Odds_Ratio_from_RAREMETALWORKER_output | '''Calculate Odds Ratio from RAREMETALWORKER output''']].
== Software Specifications ==
== Software Specifications ==
For detailed description of command options, please go to [[RAREMETALWORKER_command_reference | '''command reference''']].
For detailed description of command options, please go to [[RAREMETALWORKER_command_reference | '''command reference''']].
Options:
Input Files : --ped [], --dat [], --vcf [], --dosage, --noeof
Output Files : --prefix [], --LDwindow [1000000], --zip, --thin,
--labelHits
VC Options : --vcX, --separateX
Trait Options : --makeResiduals, --inverseNormal, --traitName []
Model Options : --recessive, --dominant
Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [],
--kinSave
Kinship Options : --kinMaf [0.05], --kinMiss [0.05]
Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044],
--maleLabel [1], --femaleLabel [2]
others : --cpu [1], --kinOnly,
--geneMap [../data/refFlat_hg19.txt]
PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
===INPUT FILE FORMAT===
===INPUT FILE FORMAT===
* When PED file has genotypes saved, there is no need for a VCF file as input.
* When PED file has genotypes saved, there is no need for a VCF file as input.
* RMW takes PED/DAT file in Merlin format. Please refer to [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.
* RMW takes PED/DAT file in Merlin format. Please refer to [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.
* PED file requires "dummy" parents to be included in the pedigree file. To check the integrity of your PED/DAT file, please use [http://www.sph.umich.edu/csg/abecasis/PedStats '''pedstats''']. To add dummy parents into the pedigree, please use the [[Media:Script.tgz | '''perl script''']].
* An example PED file is in the following:
* An example PED file is in the following:
1 1 0 0 1 1.5 1 23 A A A A A A A A A A
1 1 0 0 1 1.5 1 23 A A A A A A A A A A
* '''Markers in PED and DAT file must be sorted by chromosome and position.'''
* '''Markers in PED and DAT file must be sorted by chromosome and position.'''
* Covariate and trait values are saved in PED file. Covariate and trait descriptions are saved in DAT file.
* Covariate and trait values are saved in PED file. Covariate and trait descriptions are saved in DAT file. Note that you must specify <code>--makeResiduals</code> in order to adjust the covariates out of the phenotype. See [[RAREMETALWORKER#Example_Command_Lines | Example Command Lines]] for examples and [[RAREMETALWORKER_command_reference#Trait_Options | Trait Options]] for more information.
==== VCF File ====
==== VCF File ====
* If --zip option is used, then the following will be generated automatically:
* If --zip option is used, then the following will be generated automatically:
prefix.traitName.singlevar.score.txt.gz
prefix.traitName.singlevar.score.txt.gz
prefix.traitName.singlevar.score.txt.gz.tbi
prefix.traitName.singlevar.cov.txt.gz
prefix.traitName.singlevar.cov.txt.gz
prefix.traitName.singlevar.cov.txt.gz.tbi
prefix.singlevar.log
prefix.singlevar.log
* In the file with summary statistics named prefix.traitName.singlevar.score.txt contains summary statistics that are needed by Rare-Metal. An example is shown in below:
* In the file with summary statistics named prefix.traitName.singlevar.score.txt contains summary statistics that are needed by Rare-Metal. An example is shown in below:
LDL mean= -0.00, variance= 1.00, heritability= 34.30
CHR POS REF_ALLELE ALT_ALLELE INFORMATIVE_N FOUNDER_AF ALL_AF INFORMATIVE_AC HWE_PVALUE STAT ALT_ALLELE_EFFSIZE PVALUE
10 45410002 G A 6103 0.0341589 0.0341589 410 0.165893 126.205 0.309798 4.03074e-10
10 45410002 G A 6103 0.034159 0.034159 410 0.165893 126.2050 0.309798 4.030740e-10
19 45412079 G A 6103 0.0368124 0.0368124 434 0.714645 -265.84 -0.587356 7.87851e-36
19 45412079 G A 6103 0.036812 0.036812 434 0.714645 -265.8400 -0.587356 7.878510e-36
19 45414451 G A 6103 0.444989 0.444989 5312 0.0759271 -26.1212 -0.00837122 0.640058
19 45414451 G A 6103 0.444989 0.444989 5312 0.075927 -26.1212 -0.008371 6.400580e-01
* pvalues from the above output are from the family-based single variant score test.
* pvalues from the above output are from the family-based single variant score test.
* prefix.traitName.singlevar.cov.txt contains the LD matrix among a variant and the adjacent markers within a prefixed-sized window. The default window size is 1MB. It has the following format:
* prefix.traitName.singlevar.cov.txt contains the LD matrix among a variant and the adjacent markers within a prefixed-sized window. The default window size is 1MB. It has the following format:
CHR POS VAR_POS_IN_WINDOW LD_MATRIX
1 762320 762320,865628,865665,878744,879381,1560000 0.0359084,-0.000242112,-0.00125797,-0.000993422,-0.000344509,-0.00017077,
1 865628 865628,865665,878744,879381,1560000,1864659 0.419804,-0.0103663,-0.00635265,0.0594056,0.0534505,-0.00462183,
1 878744 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05,
=====Genomic Relationship Matrix (GRM)=====
=====Genomic Relationship Matrix (GRM)=====
* Once --kinGeno --kinSave --prefix options are requested, you would expect to see a GRM generated (compressed by gzip) with name yourprefix.Empirical.Kinship.gz. If --prefix option is not used, then the file name is Empirical.Kinship.gz.
* Once --kinGeno --kinSave --prefix options are requested, you would expect to see a GRM generated (compressed by gzip) with name yourprefix.Empirical.Kinship.gz. If --prefix option is not used, then the file name is Empirical.Kinship.gz.
* If --vcX --kinGeno --kinSave --prefix options are requested, besides the autosomal GRM, you would also expect to see a separate GRM for chromosome X saved (compressed by gzip also) under the name yourprefix.Empirical.KinshipX.gz.
* If --vcX --kinGeno --kinSave --prefix options are requested, besides the autosomal GRM, you would also expect to see a separate GRM for chromosome X saved (compressed by gzip also) under the name yourprefix.Empirical.KinshipX.gz.
* The GRMs are generated based on all genotyped individuals included in the PED file; samples with missing phenotype or missing covariates are not excluded from GRMs. This feature makes GRMs reusable if you have multiple traits to analyze in separate runs. You can simple use --kinFile option (--kinxFile option if you have X chromosome GRM together with --vcX option issued) to reuse the pre-saved GRMs.
* The GRMs are generated based on all genotyped individuals included in the PED file; samples with missing phenotype or missing covariates are not excluded from GRMs. This feature makes GRMs reusable if you have multiple traits to analyze in separate runs. You can simplely use --kinFile option (--kinxFile option if you have X chromosome GRM together with --vcX option issued) to reuse the pre-saved GRMs.
* The format for both autosomal and chromosome X GRMs are the same. The first row has all sample IDs (sample size=N) listed. The rest of the file is a symmetric matrix with dimention ''NxN'', and element ''ij'' of this matrix represents the kinship between the <math>i^{th}</math> and the <math>j^{th}</math> sample whose ID can be found from the first row.
* The format for both autosomal and chromosome X GRMs are the same. The first row has all sample IDs (sample size=N) listed. The rest of the file is a symmetric matrix with dimention ''NxN'', and element ''ij'' of this matrix represents the kinship between the <math>i^{th}</math> and the <math>j^{th}</math> sample whose ID can be found from the first row.
* For details about GRM calculation, please refer to [[RAREMETALWORKER_method | '''method''']].
* For details about GRM calculation, please refer to [[RAREMETALWORKER_method | '''method''']].
[http://genome.sph.umich.edu/wiki/Tutorial:_RareMETAL '''RAREMETAL and RAREMETALWORKER Tutorial''']
[http://genome.sph.umich.edu/wiki/Tutorial:_RareMETAL '''RAREMETAL and RAREMETALWORKER Tutorial''']
